bcl2fastq.py - Wrapper that outputs fastq files from bcl files¶
- Tags
BCL FASTQ Conversion
Purpose¶
Convert the raw data from an Illumina Sequencing Run to fastq formatted files.
Usage¶
Example:
python bcl2fastq.py -p "--runfolder-dir <RunFolder>"
This command demultiplexes and converts BCL files in the given run folder directory. All arguments for Illumina’s bcl2fastq software must be given with the -p argument. Type:
python bcl2fastq.py --help
for command line help.
Documentation¶
Converts BCL files in a given run folder to fastq.
Command line options¶
--arguments
Supply arguments to be passed to Illumia’s bcl2fastq software.
--output-dir
Required if using –fastqc.
--fastqc
After converting BCL files, run all fastq files in FastQC.
--fastqc-options
Supply arguments to be passed to FastQC.
--bcl2fastq-help
Prints help for Illumina’s bcl2fastq software.
usage: bcl2fastq [-h] [-p ARGUMENTS] [-o OUTPUT] [-f] [-F FASTQC_OPTIONS] [-H]
[--timeit TIMEIT_FILE] [--timeit-name TIMEIT_NAME]
[--timeit-header] [--random-seed RANDOM_SEED] [-v LOGLEVEL]
[--log-config-filename LOG_CONFIG_FILENAME]
[--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
[-E STDERR] [-S STDOUT]
bcl2fastq: error: argument -?: expected one argument